Source: ncbi-acc-download Version: 0.2.7-1 Severity: important Tags: ftbfs Dear Maintainer,
I am trying to assess the side effects of an upgrade of the package python-biopython to 1.79 to its reverse dependencies. Pseudo-excuses look alright, except for ncbi-acc-download [1]. [1]: https://release.debian.org/britney/pseudo-excuses-experimental.html [2]: https://ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz The full log [2] shows variations around the following symptom: __________________ test_download_wgs_parts_supercontig_retry ___________________ req = <requests_mock.mocker.Mocker object at 0x7fc14613fb20> def test_download_wgs_parts_supercontig_retry(req): cfg = Config(format="genbank") supercontig = open(full_path('supercontig.gbk'), 'rt') req.get(ENTREZ_URL, response_list=[ {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, {"body": open(full_path('supercontig_full.gbk'), 'rt')} ]) outhandle = wgs.download_wgs_parts(supercontig, cfg) supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') > assert outhandle.getvalue() == supercontig_full.read() E AssertionError: assert 'LOCUS ...671808)\n//\n' == 'LOCUS ...ccctaac\n//\n' E - LOCUS NC_007194 60 bp DNA linear CON 03-APR-2018 E ? ^^^^^^^ ^^ ^^^ ^^ E + LOCUS NC_007194 4918979 bp DNA linear CON 11-NOV-2009 E ? ^^^^^^^ ^^ ^^^ ^^ E DEFINITION Aspergillus fumigatus Af293 chromosome 1, whole genome shotgun E sequence. E ACCESSION NC_007194... E E ...Full output truncated (22 lines hidden), use '-vv' to show test_wgs.py:145: AssertionError To be honest, I don't know whether this is caused by a bug in biopython, or if it could be normal from ncbi-acc-download to issue a slightly different output. Testing against biopython 1.78 does not raise that issue. Since the test suite is run at build time, ncbi-acc-download would also fail to build from source if python-biopython were to be upgraded, hence the tag. Note that I think the package downloads resources from the Internet during the test at build time too, so would might be a serious policy violation, but I haven't checked for sure yet. Kind Regards, -- Étienne Mollier <emoll...@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/4, please excuse my verbosity.
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